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source: trunk/Mars/mcore/ofits.h@ 17301

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Last change on this file since 17301 was 17298, checked in by lyard, 11 years ago
Fixed wrong header bug
File size: 33.1 KB

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1	#ifndef MARS_ofits
2	#define MARS_ofits
3
4	#include <string>
5	#include <string.h>
6	#include <algorithm>
7	#include <sstream>
8	#include <iostream>
9	#include <fstream>
10	#include <iomanip>
11	#include <vector>
12	#include <algorithm>
13	#include <stdexcept>
14
15	#ifdef __CINT__
16	#define off_t size_t
17	#endif
18
19	#ifndef __MARS__
20	#ifndef gLog
21	#define gLog std::cerr
22	#define ___err___ ""
23	#define ___warn___ ""
24	#define ___all___ ""
25	#endif
26	#else
27	#include "MLog.h"
28	#include "MLogManip.h"
29	#define ___err___ err
30	#define ___warn___ warn
31	#define ___all___ all
32	#endif
33
34	#include "FITS.h"
35	#include "checksum.h"
36
37	// Sloppy: allow / <--- left
38	// allow all characters (see specs for what is possible)
39
40	// units: m kg s rad sr K A mol cd Hz J W V N Pa C Ohm S F Wb T Hlm lx
41
42	class ofits : public std::ofstream
43	{
44	public:
45	struct Key
46	{
47	std::string key;
48	bool delim;
49	std::string value;
50	std::string comment;
51	std::string fitsString;
52
53	off_t offset; // offset in file
54
55	bool changed; // For closing the file
56
57	Key(const std::string &k="") : key(k), delim(false), fitsString(""), offset(0), changed(true) { }
58
59	std::string Trim(const std::string &str)
60	{
61	// Trim Both leading and trailing spaces
62	const size_t first = str.find_first_not_of(' '); // Find the first character position after excluding leading blank spaces
63	const size_t last = str.find_last_not_of(' '); // Find the first character position from reverse af
64
65	// if all spaces or empty return an empty string
66	if (std::string::npos==first \|\| std::string::npos==last)
67	return std::string();
68
69	return str.substr(first, last-first+1);
70	}
71
72	bool FormatKey()
73	{
74	key = Trim(key);
75	if (key.empty())
76	{
77	#ifdef __EXCEPTIONS
78	throw std::runtime_error("Key name empty.");
79	#else
80	gLog << ___err___ << "ERROR - Key name empty." << std::endl;
81	return false;
82	#endif
83	}
84	if (key.size()>8)
85	{
86	std::ostringstream sout;
87	sout << "Key '" << key << "' exceeds 8 bytes.";
88	#ifdef __EXCEPTIONS
89	throw std::runtime_error(sout.str());
90	#else
91	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
92	return false;
93	#endif
94	}
95
96	//transform(key.begin(), key.end(), key.begin(), toupper);
97
98	for (std::string::const_iterator c=key.cbegin(); c<key.cend(); c++)
99	if ((c<'A' \|\| c>'Z') && (c<'0' \|\| c>'9') && c!='-' && c!='_')
100	{
101	std::ostringstream sout;
102	sout << "Invalid character '" << *c << "' found in key '" << key << "'";
103	#ifdef __EXCEPTIONS
104	throw std::runtime_error(sout.str());
105	#else
106	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
107	return false;
108	#endif
109	}
110
111	return true;
112	}
113
114	bool FormatComment()
115	{
116	comment = Trim(comment);
117
118	for (std::string::const_iterator c=key.cbegin(); c<key.cend(); c++)
119	if (c<32 \|\| c>126)
120	{
121	std::ostringstream sout;
122	sout << "Invalid character '" << c << "' [" << int(c) << "] found in comment '" << comment << "'";
123	#ifdef __EXCEPTIONS
124	throw std::runtime_error(sout.str());
125	#else
126	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
127	return false;
128	#endif
129	}
130
131	return true;
132	}
133
134	bool check(bool trim=false)
135	{
136	if (!FormatKey())
137	return false;
138
139	if (!FormatComment())
140	return false;
141
142	size_t sz = CalcSize();
143	if (sz<=80)
144	return true;
145
146	if (!trim)
147	{
148	std::ostringstream sout;
149	sout << "Size " << sz << " of entry for key '" << key << "' exceeds 80 characters.";
150	#ifdef __EXCEPTIONS
151	throw std::runtime_error(sout.str());
152	#else
153	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
154	#endif
155	return false;
156	}
157
158	//looks like something went wrong. Maybe entry is too long ?
159	//try to remove the comment
160	comment = "";
161
162	sz = CalcSize();
163	if (sz<=80)
164	{
165	#ifndef __EXCEPTIONS
166	std::ostringstream sout;
167	sout << "Size " << sz << " of entry for key '" << key << "' exceeds 80 characters... removed comment.";
168	gLog << ___warn___ << "WARNING - " << sout.str() << std::endl;
169	#endif
170	return true;
171	}
172
173	std::ostringstream sout;
174	sout << "Size " << sz << " of entry for key '" << key << "' exceeds 80 characters even without comment.";
175	#ifdef __EXCEPTIONS
176	throw std::runtime_error(sout.str());
177	#else
178	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
179	return false;
180	#endif
181	}
182
183	size_t CalcSize() const
184	{
185	if (!delim)
186	return 10+comment.size();
187
188	return 10 + (value.size()<20?20:value.size()) + 3 + comment.size();
189	}
190
191	std::string Compile()
192	{
193
194	if (fitsString != "")
195	return fitsString;
196
197	std::ostringstream sout;
198	sout << std::left << std::setw(8) << key;
199
200	if (!delim)
201	{
202	sout << " " << comment;
203	return sout.str();
204	}
205
206	sout << "= ";
207	sout << (!value.empty() && value[0]=='\''?std::left:std::right);
208	sout << std::setw(20) << value << std::left;
209
210	if (!comment.empty())
211	sout << " / " << comment;
212
213	return sout.str();
214	}
215
216	Checksum checksum;
217
218	void Out(std::ofstream &fout)
219	{
220	if (!changed)
221	return;
222
223	std::string str = Compile();
224	str.insert(str.end(), 80-str.size(), ' ');
225
226	if (offset==0)
227	offset = fout.tellp();
228
229	//cout << "Write[" << offset << "]: " << key << "/" << value << endl;
230
231	fout.seekp(offset);
232	fout << str;
233
234	checksum.reset();
235	checksum.add(str.c_str(), 80);
236
237	changed = false;
238	}
239	/*
240	void Out(ostream &out)
241	{
242	std::string str = Compile();
243
244	str.insert(str.end(), 80-str.size(), ' ');
245
246	out << str;
247	changed = false;
248	}*/
249	};
250
251	private:
252	std::vector<Key> fKeys;
253
254	std::vector<Key>::iterator findkey(const std::string &key)
255	{
256	for (auto it=fKeys.begin(); it!=fKeys.end(); it++)
257	if (key==it->key)
258	return it;
259
260	return fKeys.end();
261	}
262
263	bool Set(const std::string &key="", bool delim=false, const std::string &value="", const std::string &comment="")
264	{
265	// If no delimit add the row no matter if it alread exists
266	if (delim)
267	{
268	// if the row already exists: update it
269	auto it = findkey(key);
270	if (it!=fKeys.end())
271	{
272	it->value = value;
273	it->changed = true;
274	return true;
275	}
276	}
277
278	if (fTable.num_rows>0)
279	{
280	std::ostringstream sout;
281	sout << "No new header key can be defined, rows were already written to the file... ignoring new key '" << key << "'";
282	#ifdef __EXCEPTIONS
283	throw std::runtime_error(sout.str());
284	#else
285	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
286	return false;
287	#endif
288	}
289
290	Key entry;
291
292	entry.key = key;
293	entry.delim = delim;
294	entry.value = value;
295	entry.comment = comment;
296	entry.offset = 0;
297	entry.changed = true;
298
299	if (!entry.check(fCommentTrimming))
300	return false;
301
302	fKeys.push_back(entry);
303	return true;
304	}
305
306	protected:
307	struct Table
308	{
309	off_t offset;
310
311	size_t bytes_per_row;
312	size_t num_rows;
313	size_t num_cols;
314
315	struct Column
316	{
317	std::string name;
318	size_t offset;
319	size_t num;
320	size_t size;
321	char type;
322	};
323
324	std::vector<Column> cols;
325
326	Table() : offset(0), bytes_per_row(0), num_rows(0), num_cols(0)
327	{
328	}
329	};
330
331
332	Table fTable;
333
334	std::vector<char> fOutputBuffer;
335
336	std::vector<Table::Column>::const_iterator findcol(const std::string &name)
337	{
338	for (auto it=fTable.cols.cbegin(); it!=fTable.cols.cend(); it++)
339	if (name==it->name)
340	return it;
341
342	return fTable.cols.cend();
343	}
344
345	Checksum fDataSum;
346	Checksum fHeaderSum;
347
348	bool fCommentTrimming;
349	bool fManualExtName;
350
351	public:
352	ofits() : fCommentTrimming(false),
353	fManualExtName(false)
354	{
355	}
356	ofits(const char *fname) : std::ofstream(),
357	fCommentTrimming(false),
358	fManualExtName(false)
359	{
360	this->open(fname);
361	}
362	virtual ~ofits() { if (is_open()) close(); }
363
364	virtual void open(const char * filename, bool addEXTNAMEKey=true)
365	{
366	fDataSum = 0;
367	fHeaderSum = 0;
368
369	fTable = Table();
370	fKeys.clear();
371
372	SetStr("XTENSION", "BINTABLE", "binary table extension");
373	SetInt("BITPIX", 8, "8-bit bytes");
374	SetInt("NAXIS", 2, "2-dimensional binary table");
375	SetInt("NAXIS1", 0, "width of table in bytes");
376	SetInt("NAXIS2", 0, "number of rows in table");
377	SetInt("PCOUNT", 0, "size of special data area");
378	SetInt("GCOUNT", 1, "one data group (required keyword)");
379	SetInt("TFIELDS", 0, "number of fields in each row");
380	if (addEXTNAMEKey)
381	SetStr("EXTNAME", "", "name of extension table");
382	else
383	fManualExtName = true;
384	SetStr("CHECKSUM", "0000000000000000", "Checksum for the whole HDU");
385	SetStr("DATASUM", " 0", "Checksum for the data block");
386
387	std::ofstream::open(filename);
388	}
389
390	void AllowCommentsTrimming(bool allow)
391	{
392	fCommentTrimming = allow;
393	}
394	//Etienne: required to enable 1 to 1 reconstruction of files
395	bool SetKeyComment(const std::string& key, const std::string& comment)
396	{
397	auto it = findkey(key);
398	if (it==fKeys.end())
399	return false;
400	it->comment = comment;
401	it->changed = true;
402	return true;
403	}
404	bool SetKeyFromFitsString(const std::string& fitsString)
405	{
406	if (fTable.num_rows>0)
407	{
408	std::ostringstream sout;
409	sout << "No new header key can be defined, rows were already written to the file... ignoring new key '" << fitsString << "'";
410	#ifdef __EXCEPTIONS
411	throw std::runtime_error(sout.str());
412	#else
413	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
414	return false;
415	#endif
416	}
417
418	Key entry;
419	entry.fitsString = fitsString;
420	entry.changed = true;
421	fKeys.push_back(entry);
422	return true;
423	}
424	bool SetRaw(const std::string &key, const std::string &val, const std::string &comment)
425	{
426	return Set(key, true, val, comment);
427	}
428
429	bool SetBool(const std::string &key, bool b, const std::string &comment="")
430	{
431	return Set(key, true, b?"T":"F", comment);
432	}
433
434	bool AddEmpty(const std::string &key, const std::string &comment="")
435	{
436	return Set(key, true, "", comment);
437	}
438
439	bool SetStr(const std::string &key, std::string s, const std::string &comment="")
440	{
441	for (uint i=0; i<s.length(); i++)
442	if (s[i]=='\'')
443	s.insert(i++, "\'");
444
445	return Set(key, true, "'"+s+"'", comment);
446	}
447
448	bool SetInt(const std::string &key, int64_t i, const std::string &comment="")
449	{
450	std::ostringstream sout;
451	sout << i;
452
453	return Set(key, true, sout.str(), comment);
454	}
455
456	bool SetFloat(const std::string &key, double f, int p, const std::string &comment="")
457	{
458	std::ostringstream sout;
459
460	if (p<0)
461	sout << std::setprecision(-p) << fixed;
462	if (p>0)
463	sout << std::setprecision(p);
464	if (p==0)
465	sout << std::setprecision(f>1e-100 && f<1e100 ? 15 : 14);
466
467	sout << f;
468
469	std::string str = sout.str();
470
471	replace(str.begin(), str.end(), 'e', 'E');
472
473	if (str.find_first_of('E')==std::string::npos && str.find_first_of('.')==std::string::npos)
474	str += ".";
475
476	return Set(key, true, str, comment);
477	}
478
479	bool SetFloat(const std::string &key, double f, const std::string &comment="")
480	{
481	return SetFloat(key, f, 0, comment);
482	}
483
484	bool SetHex(const std::string &key, uint64_t i, const std::string &comment="")
485	{
486	std::ostringstream sout;
487	sout << std::hex << "0x" << i;
488	return SetStr(key, sout.str(), comment);
489	}
490
491	bool AddComment(const std::string &comment)
492	{
493	return Set("COMMENT", false, "", comment);
494	}
495
496	bool AddHistory(const std::string &comment)
497	{
498	return Set("HISTORY", false, "", comment);
499	}
500
501	void End()
502	{
503	Set("END");
504	while (fKeys.size()%36!=0)
505	fKeys.emplace_back();
506	}
507
508	std::string CommentFromType(char type)
509	{
510	std::string comment;
511
512	switch (type)
513	{
514	case 'L': comment = "[1-byte BOOL]"; break;
515	case 'A': comment = "[1-byte CHAR]"; break;
516	case 'B': comment = "[1-byte BOOL]"; break;
517	case 'I': comment = "[2-byte INT]"; break;
518	case 'J': comment = "[4-byte INT]"; break;
519	case 'K': comment = "[8-byte INT]"; break;
520	case 'E': comment = "[4-byte FLOAT]"; break;
521	case 'D': comment = "[8-byte FLOAT]"; break;
522	case 'Q': comment = "[var. Length]"; break;
523	}
524
525	return comment;
526	}
527
528	uint32_t SizeFromType(char type)
529	{
530	size_t size = 0;
531
532	switch (type)
533	{
534	case 'L': size = 1; break;
535	case 'A': size = 1; break;
536	case 'B': size = 1; break;
537	case 'I': size = 2; break;
538	case 'J': size = 4; break;
539	case 'K': size = 8; break;
540	case 'E': size = 4; break;
541	case 'D': size = 8; break;
542	case 'Q': size = 16; break;
543	}
544
545	return size;
546	}
547	//ETIENNE to be able to restore the file 1 to 1, I must restore the header keys myself
548	virtual bool AddColumn(uint32_t cnt, char typechar, const std::string &name, const std::string &unit, const std::string &comment="", bool addHeaderKeys=true)
549	{
550	if (tellp()<0)
551	{
552	std::ostringstream sout;
553	sout << "File not open... ignoring column '" << name << "'";
554	#ifdef __EXCEPTIONS
555	throw std::runtime_error(sout.str());
556	#else
557	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
558	return false;
559	#endif
560	}
561
562	if (tellp()>0)
563	{
564	std::ostringstream sout;
565	sout << "Header already written, no new column can be defined... ignoring column '" << name << "'";
566	#ifdef __EXCEPTIONS
567	throw std::runtime_error(sout.str());
568	#else
569	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
570	return false;
571	#endif
572	}
573
574	if (findcol(name)!=fTable.cols.cend())
575	{
576	std::ostringstream sout;
577	sout << "A column with the name '" << name << "' already exists.";
578	#ifdef __EXCEPTIONS
579	throw std::runtime_error(sout.str());
580	#else
581	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
582	return false;
583	#endif
584	}
585
586	typechar = toupper(typechar);
587
588	static const std::string allow("LABIJKEDQ");
589	if (std::find(allow.cbegin(), allow.cend(), typechar)==allow.end())
590	{
591	std::ostringstream sout;
592	sout << "Column type '" << typechar << "' not supported.";
593	#ifdef __EXCEPTIONS
594	throw std::runtime_error(sout.str());
595	#else
596	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
597	return false;
598	#endif
599	}
600
601	std::ostringstream type;
602	type << cnt;
603	if (typechar=='Q')
604	type << "QB";
605	else
606	type << typechar;
607
608	fTable.num_cols++;
609
610	if (addHeaderKeys)
611	{
612	const std::string nc = std::to_string(fTable.num_cols);
613
614	SetStr("TFORM"+nc, type.str(), "format of "+name+" "+CommentFromType(typechar));
615	SetStr("TTYPE"+nc, name, comment);
616	if (!unit.empty())
617	SetStr("TUNIT"+nc, unit, "unit of "+name);
618	}
619	size_t size = SizeFromType(typechar);
620
621	Table::Column col;
622
623	col.name = name;
624	col.type = typechar;
625	col.num = cnt;
626	col.size = size;
627	col.offset = fTable.bytes_per_row;
628
629	fTable.cols.push_back(col);
630
631	fTable.bytes_per_row += size*cnt;
632
633	// Align to four bytes
634	fOutputBuffer.resize(fTable.bytes_per_row + 4-fTable.bytes_per_row%4);
635
636	return true;
637	}
638
639	virtual bool AddColumn(const FITS::Compression&, uint32_t cnt, char typechar, const std::string& name, const std::string& unit, const std::string& comment="", bool addHeaderKeys=true)
640	{
641	return AddColumn(cnt, typechar, name, unit, comment, addHeaderKeys);
642	}
643
644	bool AddColumnShort(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
645	{ return AddColumn(cnt, 'I', name, unit, comment); }
646	bool AddColumnInt(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
647	{ return AddColumn(cnt, 'J', name, unit, comment); }
648	bool AddColumnLong(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
649	{ return AddColumn(cnt, 'K', name, unit, comment); }
650	bool AddColumnFloat(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
651	{ return AddColumn(cnt, 'E', name, unit, comment); }
652	bool AddColumnDouble(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
653	{ return AddColumn(cnt, 'D', name, unit, comment); }
654	bool AddColumnChar(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
655	{ return AddColumn(cnt, 'A', name, unit, comment); }
656	bool AddColumnByte(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
657	{ return AddColumn(cnt, 'B', name, unit, comment); }
658	bool AddColumnBool(uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
659	{ return AddColumn(cnt, 'L', name, unit, comment); }
660
661	bool AddColumnShort(const std::string &name, const std::string &unit="", const std::string &comment="")
662	{ return AddColumn(1, 'I', name, unit, comment); }
663	bool AddColumnInt(const std::string &name, const std::string &unit="", const std::string &comment="")
664	{ return AddColumn(1, 'J', name, unit, comment); }
665	bool AddColumnLong(const std::string &name, const std::string &unit="", const std::string &comment="")
666	{ return AddColumn(1, 'K', name, unit, comment); }
667	bool AddColumnFloat(const std::string &name, const std::string &unit="", const std::string &comment="")
668	{ return AddColumn(1, 'E', name, unit, comment); }
669	bool AddColumnDouble(const std::string &name, const std::string &unit="", const std::string &comment="")
670	{ return AddColumn(1, 'D', name, unit, comment); }
671	bool AddColumnChar(const std::string &name, const std::string &unit="", const std::string &comment="")
672	{ return AddColumn(1, 'A', name, unit, comment); }
673	bool AddColumnByte(const std::string &name, const std::string &unit="", const std::string &comment="")
674	{ return AddColumn(1, 'B', name, unit, comment); }
675	bool AddColumnBool(const std::string &name, const std::string &unit="", const std::string &comment="")
676	{ return AddColumn(1, 'L', name, unit, comment); }
677
678	bool AddColumnShort(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
679	{ return AddColumn(comp, cnt, 'I', name, unit, comment); }
680	bool AddColumnInt(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
681	{ return AddColumn(comp, cnt, 'J', name, unit, comment); }
682	bool AddColumnLong(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
683	{ return AddColumn(comp, cnt, 'K', name, unit, comment); }
684	bool AddColumnFloat(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
685	{ return AddColumn(comp, cnt, 'E', name, unit, comment); }
686	bool AddColumnDouble(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
687	{ return AddColumn(comp, cnt, 'D', name, unit, comment); }
688	bool AddColumnChar(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
689	{ return AddColumn(comp, cnt, 'A', name, unit, comment); }
690	bool AddColumnByte(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
691	{ return AddColumn(comp, cnt, 'B', name, unit, comment); }
692	bool AddColumnBool(const FITS::Compression &comp, uint32_t cnt, const std::string &name, const std::string &unit="", const std::string &comment="")
693	{ return AddColumn(comp, cnt, 'L', name, unit, comment); }
694
695	bool AddColumnShort(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
696	{ return AddColumn(comp, 1, 'I', name, unit, comment); }
697	bool AddColumnInt(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
698	{ return AddColumn(comp, 1, 'J', name, unit, comment); }
699	bool AddColumnLong(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
700	{ return AddColumn(comp, 1, 'K', name, unit, comment); }
701	bool AddColumnFloat(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
702	{ return AddColumn(comp, 1, 'E', name, unit, comment); }
703	bool AddColumnDouble(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
704	{ return AddColumn(comp, 1, 'D', name, unit, comment); }
705	bool AddColumnChar(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
706	{ return AddColumn(comp, 1, 'A', name, unit, comment); }
707	bool AddColumnByte(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
708	{ return AddColumn(comp, 1, 'B', name, unit, comment); }
709	bool AddColumnBool(const FITS::Compression &comp, const std::string &name, const std::string &unit="", const std::string &comment="")
710	{ return AddColumn(comp, 1, 'L', name, unit, comment); }
711
712	/*
713	bool AddKey(string key, double d, const std::string &comment)
714	{
715	ostringstream out;
716	out << d;
717
718	std::string s = out.str();
719
720	replace(s.begin(), s.end(), "e", "E");
721
722	return AddKey(key, s, comment);
723	}*/
724
725
726	Checksum WriteHeader(std::ofstream &fout)
727	{
728	Checksum sum;
729	uint32_t count=0;
730	for (auto it=fKeys.begin(); it!=fKeys.end(); it++)
731	{
732	it->Out(fout);
733	sum += it->checksum;
734	count++;
735	}
736	fout.flush();
737
738	return sum;
739	}
740
741	Checksum WriteHeader()
742	{
743	return WriteHeader(*this);
744	}
745
746	void FlushHeader()
747	{
748	const off_t pos = tellp();
749	WriteHeader();
750	seekp(pos);
751	}
752
753	Checksum WriteFitsHeader()
754	{
755	ofits h;
756
757	h.SetBool("SIMPLE", true, "file does conform to FITS standard");
758	h.SetInt ("BITPIX", 8, "number of bits per data pixel");
759	h.SetInt ("NAXIS", 0, "number of data axes");
760	h.SetBool("EXTEND", true, "FITS dataset may contain extensions");
761	h.SetStr ("CHECKSUM","0000000000000000", "Checksum for the whole HDU");
762	h.SetStr ("DATASUM", " 0", "Checksum for the data block");
763	h.AddComment("FITS (Flexible Image Transport System) format is defined in 'Astronomy");
764	h.AddComment("and Astrophysics', volume 376, page 359; bibcode: 2001A&A...376..359H");
765	h.End();
766
767	const Checksum sum = h.WriteHeader(*this);
768
769	h.SetStr("CHECKSUM", sum.str());
770
771	const size_t offset = tellp();
772	h.WriteHeader(*this);
773	seekp(offset);
774
775	return sum;
776	}
777
778	virtual bool WriteDrsOffsetsTable ()
779	{
780	return true;
781	}
782
783	virtual bool WriteCatalog()
784	{
785	return true;
786	}
787
788	virtual bool WriteTableHeader(const char *name="DATA")
789	{
790	if (tellp()>0)
791	{
792	#ifdef __EXCEPTIONS
793	throw std::runtime_error("File not empty anymore.");
794	#else
795	gLog << ___err___ << "ERROR - File not empty anymore." << std::endl;
796	return false;
797	#endif
798	}
799
800	fHeaderSum = WriteFitsHeader();
801
802	WriteDrsOffsetsTable();
803
804	if (!fManualExtName)
805	SetStr("EXTNAME", name);
806	SetInt("NAXIS1", fTable.bytes_per_row);
807	SetInt("TFIELDS", fTable.cols.size());
808
809	End();
810
811	WriteHeader();
812
813	WriteCatalog();
814
815	return good();
816	}
817
818	template<size_t N>
819	void revcpy(char dest, const char src, int num)
820	{
821	const char pend = src + numN;
822	for (const char *ptr = src; ptr<pend; ptr+=N, dest+=N)
823	std::reverse_copy(ptr, ptr+N, dest);
824	}
825
826	virtual uint32_t GetBytesPerRow() const { return fTable.bytes_per_row; }
827
828	virtual bool WriteRow(const void *ptr, size_t cnt, bool byte_swap=true)
829	{
830	// FIXME: Make sure that header was already written
831	// or write header now!
832	if (cnt!=fTable.bytes_per_row)
833	{
834	std::ostringstream sout;
835	sout << "WriteRow - Size " << cnt << " does not match expected size " << fTable.bytes_per_row;
836	#ifdef __EXCEPTIONS
837	throw std::runtime_error(sout.str());
838	#else
839	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
840	return false;
841	#endif
842	}
843
844	// For the checksum we need everything to be correctly aligned
845	const uint8_t offset = fTable.offset%4;
846
847	char *buffer = fOutputBuffer.data() + offset;
848
849	auto ib = fOutputBuffer.begin();
850	auto ie = fOutputBuffer.rbegin();
851	*ib++ = 0;
852	*ib++ = 0;
853	*ib++ = 0;
854	*ib = 0;
855
856	*ie++ = 0;
857	*ie++ = 0;
858	*ie++ = 0;
859	*ie = 0;
860
861	if (!byte_swap)
862	memcpy(buffer, ptr, cnt);
863	else
864	{
865	for (auto it=fTable.cols.cbegin(); it!=fTable.cols.cend(); it++)
866	{
867	const char src = reinterpret_cast<const char>(ptr) + it->offset;
868	char *dest = buffer + it->offset;
869
870	// Let the compiler do some optimization by
871	// knowing the we only have 1, 2, 4 and 8
872	switch (it->size)
873	{
874	case 1: memcpy (dest, src, it->num*it->size); break;
875	case 2: revcpy<2>(dest, src, it->num); break;
876	case 4: revcpy<4>(dest, src, it->num); break;
877	case 8: revcpy<8>(dest, src, it->num); break;
878	}
879	}
880	}
881
882	write(buffer, cnt);
883	fDataSum.add(fOutputBuffer);
884
885	fTable.num_rows++;
886	fTable.offset += cnt;
887	return good();
888	}
889
890	template<typename N>
891	bool WriteRow(const std::vector<N> &vec)
892	{
893	return WriteRow(vec.data(), vec.size()*sizeof(N));
894	}
895
896	// Flushes the number of rows to the header on disk
897	virtual void FlushNumRows()
898	{
899	SetInt("NAXIS2", fTable.num_rows);
900	FlushHeader();
901	}
902
903	size_t GetNumRows() const { return fTable.num_rows; }
904
905	void AlignTo2880Bytes()
906	{
907	if (tellp()%(80*36)>0)
908	{
909	std::vector<char> filler(8036-tellp()%(8036));
910	write(filler.data(), filler.size());
911	}
912	}
913
914	Checksum UpdateHeaderChecksum()
915	{
916
917	std::ostringstream dataSumStr;
918	dataSumStr << fDataSum.val();
919	SetStr("DATASUM", dataSumStr.str());
920
921	const Checksum sum = WriteHeader();
922
923	//sum += headersum;
924
925	SetStr("CHECKSUM", (sum+fDataSum).str());
926
927	return WriteHeader();
928	}
929	virtual bool close()
930	{
931	if (tellp()<0)
932	return false;
933
934	AlignTo2880Bytes();
935
936	// We don't have to jump back to the end of the file
937	SetInt("NAXIS2", fTable.num_rows);
938
939
940	const Checksum chk = UpdateHeaderChecksum();
941
942	std::ofstream::close();
943
944	if ((chk+fDataSum).valid())
945	return true;
946
947	std::ostringstream sout;
948	sout << "Checksum (" << std::hex << chk.val() << ") invalid.";
949	#ifdef __EXCEPTIONS
950	throw std::runtime_error(sout.str());
951	#else
952	gLog << ___err___ << "ERROR - " << sout.str() << std::endl;
953	return false;
954	#endif
955	}
956
957	std::pair<std::string, int> GetChecksumData()
958	{
959	std::string datasum;
960	std::string checksum;
961	//cannot directly use the Get methods, because they are only in fits.h
962	for (std::vector<Key>::const_iterator it=fKeys.cbegin(); it!= fKeys.cend(); it++)
963	{
964	if (it->key == "CHECKSUM") checksum = it->value;
965	if (it->key == "DATASUM") datasum = it->value;
966	}
967	if (checksum[0] == '\'')
968	checksum = checksum.substr(1,checksum.size()-2);
969	if (datasum[0] == '\'')
970	datasum = datasum.substr(1, datasum.size()-2);
971	return std::make_pair(checksum, atoi(datasum.c_str()));
972	}
973
974	void SetDefaultKeys()
975	{
976	SetStr("TELESCOP", "FACT", "Telescope that acquired this data");
977	SetStr("CREATOR", typeid(*this).name(), "Class that wrote this file");
978	SetFloat("EXTREL", 1.0, "Release Number");
979	SetStr("COMPILED", __DATE__" "__TIME__, "Compile time");
980	SetStr("ORIGIN", "FACT", "Institution that wrote the file");
981	SetStr("TIMESYS", "UTC", "Time system");
982	SetStr("TIMEUNIT", "d", "Time given in days w.r.t. to MJDREF");
983	SetInt("MJDREF", 40587, "MJD to UNIX time (seconds since 1970/1/1)");
984	SetStr("PACKAGE", PACKAGE_NAME, "Package name");
985	SetStr("VERSION", PACKAGE_VERSION, "Package description");
986	SetStr("REVISION", REVISION, "SVN revision");
987
988	const time_t t0 = time(NULL);
989	const struct tm *tmp1 = gmtime(&t0);
990
991	std::string str(19, '\0');
992	if (tmp1 && strftime(const_cast<char*>(str.data()), 20, "%Y-%m-%dT%H:%M:%S", tmp1))
993	SetStr("DATE", str, "File creation date");
994	}
995	};
996
997	#if 0
998	#include "fits.h"
999
1000	int main()
1001	{
1002	using namespace std;
1003
1004	ofits h2("delme.fits");
1005
1006	h2.SetInt("KEY1", 1, "comment 1");
1007	h2.AddColumnInt(2, "testcol1", "counts", "My comment");
1008	h2.AddColumnInt("testcol2", "counts", "My comment");
1009	//h2.AddColumnInt("testcol2", "counts", "My comment");
1010	h2.SetInt("KEY2", 2, "comment 2");
1011
1012	/*
1013	AddFloat("X0", 0.000123456, "number of fields in each row");
1014	AddFloat("X1", 0, "number of fields in each row");
1015	AddFloat("X2", 12345, "number of fields in each row");
1016	AddFloat("X3", 123456.67890, "number of fields in each row");
1017	AddFloat("X4", 1234567890123456789.12345678901234567890, "number of fields in each row");
1018	AddFloat("X5", 1234567890.1234567890e20, "number of fields in each row");
1019	AddFloat("X6", 1234567890.1234567890e-20, "number of fields in each row");
1020	AddFloat("XB", 1234567890.1234567890e-111, "number of fields in each row");
1021	AddFloat("X7", 1e-5, "number of fields in each row");
1022	AddFloat("X8", 1e-6, "number of fields in each row");
1023	//AddStr("12345678", "123456789012345678", "12345678901234567890123456789012345678901234567");
1024	*/
1025	// -
1026
1027	h2.WriteTableHeader("TABLE_NAME");
1028
1029	for (int i=0; i<10; i++)
1030	{
1031	int j[3] = { i+10, i10, i100 };
1032	h2.WriteRow(j, 3*sizeof(i));
1033	}
1034
1035	//h2.AddColumnInt("testcol2", "counts", "My comment");
1036	//h2.SetInt("KEY3", 2, "comment 2");
1037	h2.SetInt("KEY2", 2, "comment 2xxx");
1038	h2.SetInt("KEY1", 11);
1039
1040	h2.close();
1041
1042	cout << "---" << endl;
1043
1044	fits f("delme.fits");
1045	if (!f)
1046	throw std::runtime_error("xxx");
1047
1048	cout << "Header is valid: " << f.IsHeaderOk() << endl;
1049
1050	while (f.GetNextRow());
1051
1052	cout << "File is valid: " << f.IsFileOk() << endl;
1053
1054	cout << "---" << endl;
1055
1056	return 0;
1057	}
1058	#endif
1059
1060	#endif

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